Understanding protein folding: small proteins in silico

Recent improvements in methodology and increased computer power now allow atomistic computer simulations of protein folding. We briefly review several advanced Monte Carlo algorithms that have contributed to this development. Details of folding simulations of three designed mini proteins are shown. Adding global translations and rotations has allowed us to handle multiple chains and to simulate the aggregation of six beta-amyloid fragments. In a different line of research we have developed several algorithms to predict local features from sequence. In an outlook we sketch how such biasing could extend the application spectrum of Monte Carlo simulations to structure prediction of larger proteins.     

Characterization of cellulosic fibers and fabrics by sorption/desorption

Three cellulosic substrates: lyocell (CLY), viscose (CV), and modal (CMD) in the form of fibers and fabrics were subjected to wet/dry or wash/dry treatments. The accessibility of untreated and treated substrates to water and iodine was investigated using dynamic water-vapor sorption, moisture retention, and iodine sorption methods, to study the influence of treatments on sorption-desorption hysteresis, fraction of moisture sorbed as a monomolecular layer, water retention, and iodine sorption. It was found that the sorption properties of untreated and treated substrates differed with sorbate type as well as substrate type and form.     

Functional Properties of <Emphasis Type="Italic">Lactobacillus plantarum</Emphasis> Strains Isolated from Maasai Traditional Fermented Milk Products in Kenya

Lactobacillus plantarum was the major species among the lactic acid bacterial strains isolated from traditional fermented milk of the Maasai in Kenya. Selected strains were characterized for their functional properties using in vitro standard procedures. All strains expressed acid tolerance at pH 2.0 after 2-h exposure of values that ranged from 1% to 100%, while bile tolerance of acid-stressed cells at 0.3% oxgal varied from 30% to 80%. In vitro adhesion to the mucus-secreting cell line HT 29 MTX and binding capacity to extracellular protein matrices was demonstrated for several strains. The four strains tested in a simulated stomach duodenum passage survived with recovery rates ranging from 17% to 100%. Strains were intrinsically resistant to several antibiotics tested. From these in vitro studies, a number of Lb. plantarum strains isolated from the Maasai traditional fermented milk showed probiotic potential. The strains are good candidates for multifunctional starter culture development.     

Limits to the estimation of species richness: The use of relative abundance distributions

The present study demonstrates the possibility of estimating species numbers of animal or plant communities from samples using relative abundance distributions. We use log‐abundance–species‐rank order plots and derive two new estimators that are based on log‐series and lognormal distributions. At small to moderate sample sizes these estimators appear to be more precise than previous parametric and nonparametric estimators. We test our estimators using samples from 171 published medium‐sized to large animal and plant communities taken from the literature. By this we show that our new estimators define also limits of precision.     

Species- and clone-specific responses to environmental stimuli in the cladocerans Bosmina cornuta and B. pellucida - a comparison with Daphnia

We studied the variation of small-scale swimming behaviour in eight Bosmina cornuta and ten B. pellucida clones in response to key environmental factors to test whether swimming behaviour and genotypes are linked in non-Daphnia cladocerans. We quantified (1) the short-term responses to changes in temperature, light intensity and pH, (2) the response to long-term temperature acclimation, and (3) the pH-related survival rates. Vertical swimming activity S was quantified in cuvette experiments as crossings of a line at 2 cm height per individual an hour. S differed significantly among species and conspecific clones. At any temperature, light intensity and pH tested, B. cornuta (clone variation: 40-58 crossings/ind.× h) showed a higher vertical swimming activity than B. pellucida (clone variation: 25-48 crossings/ind.× h). A short-term change of water temperature (range tested: 10-25°C) only affected S of B. cornuta, whereas that of B. pellucida remained unaltered. In contrast, S increased with rising temperature following long-term temperature acclimation (range tested: 10-20°C) in both species. Swimming activity was inversely related to the light intensity (range tested: 60-60,000 lux), but decrease of activity was stronger in B. pellucida (44 → 12 crossings/ind × h) than in B. cornuta (50 → 40 crossings/ind.× h). Short-term changes of pH (range tested: 4-6) did not influence swimming activity in any species, although a prolonged exposure (24 h) to pH 4 was lethal. Thus, Bosmina showed behavioural responses which permit to distinguish between the species and which are related to their seasonal succession and distribution pattern.     

Changes of Body Weight and Plasma Ghrelin Levels after Gastric Banding and Gastric Bypass

Objective: Ghrelin is an enteric peptide with strong orexigenic and adipogenic effects. Plasma ghrelin levels are decreased in obese subjects but increase after weight loss; this increase is not observed after Roux‐en‐Y gastric bypass (RYGB). Prospective and comparative data after adjustable silicone gastric banding (ASGB) have not been reported previously. Research Methods and Procedures: Overnight fasting plasma ghrelin concentration was measured in morbidly obese subjects at baseline and 3, 6, 12, and 24 months after ASGB (n = 8) or RYGB (n = 5) and in nonoperated controls (n = 7). Results: After RYGB, body weight (BW) decreased by 29.5 ± 5.5 kg (mean ± SE, p < 0.001), whereas plasma ghrelin failed to increase significantly (+167 ± 119 pg/mL, not significant). In contrast, after ASGB, BW decreased less (by 22.8 ± 5.9 kg; p < 0.001), and plasma ghrelin significantly increased by 377 ± 201 pg/mL (p = 0.025). Neither BW nor plasma ghrelin changed in nonoperated controls. Plasma leptin decreased in both operated groups (similarly p < 0.05) but not in nonoperated controls. Plasma growth hormone and insulin‐like growth factor 1 were not correlated with changes in plasma ghrelin concentrations. Discussion: Plasma ghrelin levels failed to increase during substantial weight loss after RYGB, but did increase in response to lesser weight loss after ASGB. These findings suggest that the plasma ghrelin response after weight loss is impaired after exclusion of major parts of the stomach and the duodenum (RYGB), and the smaller long‐term weight loss after ASGB compared with RYGB may be due, at least in part, to an absent increase in plasma ghrelin after RYGB.     

Complex regulation of gene expression, photosynthesis and sugar levels by pathogen infection in tomato

The infection of plants with pathogens results in the induction of defence reactions as well as changes in carbohydrate metabolism. On the one hand, the pathogen attempts to manipulate the carbohydrate metabolism of the plant for its own advantage. On the other, the plant has to reorganize carbon fluxes to ensure fight against the pathogen. In order to further investigate the connection between pathogen infection and carbohydrate metabolism, the effects of two types of pathogen, biotrophic and necrotrophic, on gene expression, endogenous sugar levels and photosynthesis of tomato plants were analysed. Photosynthetic gene expression was downregulated on infection with Pseudomonas syringae and Botrytis cinerea . In contrast, expression of a sink-specific gene encoding a cell wall invertase and of defence genes was induced by both pathogens. These results provide evidence for a co-regulation of defence, sink and photosynthetic gene expression in planta in response to both types of pathogen. The brassinosteroid-containing plant restorative ComCat enhanced resistance against B. cinerea and counter-regulated the repression of photosynthetic gene expression. Endogenous sugar levels decreased and the hexose to sucrose ratio increased on treatment with B. cinerea . The application of chlorophyll fluorescence imaging revealed the spatio-temporal heterogeneity of the pathogen response. At 24 h after infection, inhibition of photosynthetic electron transport was restricted to the direct vicinity of the infection site, which was surrounded by a circle of increased photosynthetic activity. The photosynthesis of the remaining leaf was not affected at this stage. These results show the usefulness of chlorophyll fluorescence imaging for the assessment of the complex spatio-temporal changes and for the definition of the areas relevant for other types of determination, e.g. gene expression.     

Aphid suppression by natural enemies in mulched cereals

Large populations of natural enemies are the basis for natural pest control. Effects of mulch on predator–prey interactions in arable fields are poorly known, despite its potential to enhance ground‐dwelling predators and thereby reduce pest infestations. We studied the densities of predators and parasitoids, and their impact on cereal aphids in the presence and absence of mulch. Released populations of the bird cherry aphid, Rhopalosiphum padi (L.) (Homoptera: Aphididae), and two naturally occurring aphid species, were monitored under experimentally reduced densities of: (i) ground‐dwelling predators, (ii) flying predators and parasitoids, and (iii) with straw mulch. The three treatments were applied in a 2 × 2 × 2 factorial design in a field of spring wheat (Triticum aestivum L.). The exclusion of ground‐dwelling predators increased aphid populations by 55% in June and 40% in July, respectively. Mulched plots had 25% lower aphid densities in June. This was presumably due to enhanced densities of spiders (Araneida) in mulched plots. The exclusion of flying predators and parasitoids led to 94% higher aphid populations in late July (109 vs. 56 individuals per 100 shoots), irrespective of mulch or ground predator manipulation. This was attributed to the larvae of gall midges Aphidoletes cf. aphidimyza (Rondani) (Diptera: Cecidomyiidae) and hoverflies (Diptera: Syrphidae). The results indicate that a scarcity of predators and a bare soil surface renders crops more susceptible to arthropod pests. Farming schemes should aim at enhancing both ground‐dwelling and flying predators for elevated levels of natural pest control.